Is it possible to have multiple physics simulations in blender game engine?
If the areas do not interact at all, can you even see them at the same time? Could you completely forget about the "other" ones while you're over in one small part of the universe?

If not, and you always need to be able to see them, you could try doing things with multiple scenes. Each simulation takes place near the origin, and the camera shifts to provide the correct view of it.

I will echo GiantCowFilms: I doubt floating point is the issue here. If I remember correctly, a 32 bit float has enough precision to work at ±1cm at the radius of earth (6000km)